1     M         0.409   0.412   0.414   0.997   1.002   0.993   0.417   0.419   0.422
2     S         0.409   0.412   0.414   0.997   1.002   0.993   0.417   0.419   0.422
3     S        -1.741  -1.624  -1.836  -1.181  -0.990  -1.475  -1.905  -1.719  -2.026
4     R         0.409   0.412   0.414   1.278   1.277   1.263   0.417   0.419   0.422
5     Q         0.409   0.412   0.414   0.664   0.680   0.671   0.417   0.419   0.422
6     G         0.409   0.412   0.414   0.535   0.552   0.547   0.417   0.419   0.422
7     G         0.409   0.412   0.414   0.535   0.552   0.547   0.417   0.419   0.422
8     K         0.409   0.412   0.414  -0.901  -0.894  -0.838   0.417   0.419   0.422
9     M        -3.303  -3.231  -3.164  -2.581  -2.465  -2.459  -3.066  -2.961  -2.857
10    K         0.409   0.412   0.414  -0.901  -0.894  -0.838   0.417   0.419   0.422
11    P         0.409   0.412   0.414   1.038   1.038   1.032   0.417   0.419   0.422
12    L         0.409   0.412   0.414   0.997   1.002   0.993   0.417   0.419   0.422
13    K         0.409   0.412   0.414  -0.901  -0.894  -0.838   0.417   0.419   0.422
14    Q         0.409   0.412   0.414   0.664   0.680   0.671   0.417   0.419   0.422
15    K         0.409   0.412   0.414  -0.901  -0.894  -0.838   0.417   0.419   0.422
16    K         0.409   0.412   0.414  -0.901  -0.894  -0.838   0.417   0.419   0.422
17    K         0.409   0.412   0.414  -0.901  -0.894  -0.838   0.417   0.419   0.422
18    Q         0.409   0.412   0.414   0.664   0.680   0.671   0.417   0.419   0.422
19    Q        -1.741  -1.857  -1.841  -1.163  -1.296  -1.265  -1.905  -2.064  -2.034
20    Q         0.409   0.412   0.414   0.664   0.680   0.671   0.417   0.419   0.422
21    D         0.409   0.412   0.414   0.956   0.966   0.953   0.417   0.419   0.422
22    L        -1.741  -1.857  -1.841  -0.889  -1.059  -1.064  -1.905  -2.064  -2.034
23    D         0.409   0.412   0.414   0.956   0.966   0.953   0.417   0.419   0.422
24    P         0.409   0.412   0.414   1.038   1.038   1.032   0.417   0.419   0.422
25    E         0.409   0.412   0.414   1.078   1.060   1.071   0.417   0.419   0.422
26    D        -1.741  -1.857  -1.841  -0.979  -1.164  -1.170  -1.905  -2.064  -2.034
27    I        -3.303  -3.231  -3.164  -2.293  -2.211  -2.182  -3.066  -2.961  -2.857
28    A         0.409   0.412   0.414   0.448   0.446   0.463   0.417   0.419   0.422
29    F        -1.741  -1.857  -1.841  -0.543  -0.718  -0.746  -1.905  -2.064  -2.034
30    K         0.409   0.412   0.414  -0.901  -0.894  -0.838   0.417   0.419   0.422
31    E         0.409   0.412   0.414   1.078   1.060   1.071   0.417   0.419   0.422
32    K         0.409   0.412   0.414  -0.901  -0.894  -0.838   0.417   0.419   0.422
33    Q         0.409   0.412   0.414   0.664   0.680   0.671   0.417   0.419   0.422
34    K         0.409   0.412   0.414  -0.901  -0.894  -0.838   0.417   0.419   0.422
35    A         0.409   0.412   0.414   0.448   0.446   0.463   0.417   0.419   0.422
36    D         0.409   0.412   0.414   0.956   0.966   0.953   0.417   0.419   0.422
37    A         0.409   0.412   0.414   0.448   0.446   0.463   0.417   0.419   0.422
38    A         0.409   0.412   0.414   0.448   0.446   0.463   0.417   0.419   0.422
39    A         0.409   0.412   0.414   0.448   0.446   0.463   0.417   0.419   0.422
40    K         0.409   0.412   0.414  -0.901  -0.894  -0.838   0.417   0.419   0.422
41    K         0.409   0.412   0.414  -0.901  -0.894  -0.838   0.417   0.419   0.422
42    A         0.409   0.412   0.414   0.448   0.446   0.463   0.417   0.419   0.422
43    L        -1.741  -1.624  -1.836  -0.979  -0.820  -1.186  -1.905  -1.719  -2.026
44    M         0.409   0.412   0.414   0.997   1.002   0.993   0.417   0.419   0.422
45    A         0.409   0.412   0.414   0.448   0.446   0.463   0.417   0.419   0.422
46    N         0.409   0.412   0.414   1.238   1.229   1.225   0.417   0.419   0.422
47    M        -3.303  -3.231  -3.164  -2.045  -1.967  -1.942  -3.066  -2.961  -2.857
48    K         0.409   0.412   0.414  -0.901  -0.894  -0.838   0.417   0.419   0.422
49    S        -1.741  -1.857  -1.841  -1.219  -1.479  -1.550  -1.905  -2.064  -2.034
50    G         0.409   0.412   0.414   0.535   0.552   0.547   0.417   0.419   0.422
51    K         0.409   0.412   0.414  -0.901  -0.894  -0.838   0.417   0.419   0.422
52    P         0.409   0.412   0.414   1.038   1.038   1.032   0.417   0.419   0.422
53    L         0.409   0.412   0.414   0.997   1.002   0.993   0.417   0.419   0.422
54    V         0.409   0.412   0.414   1.198   1.194   1.187   0.417   0.419   0.422
55    G         0.409   0.412   0.414   0.535   0.552   0.547   0.417   0.419   0.422
56    G         0.409   0.412   0.414   0.535   0.552   0.547   0.417   0.419   0.422
57    G         0.409   0.412   0.414   0.535   0.552   0.547   0.417   0.419   0.422
58    I         0.409   0.412   0.414   1.198   1.194   1.187   0.417   0.419   0.422
59    K         0.409   0.412   0.414  -0.901  -0.894  -0.838   0.417   0.419   0.422
60    K         0.409   0.412   0.414  -0.901  -0.894  -0.838   0.417   0.419   0.422
61    S         0.409   0.412   0.414   0.997   1.002   0.993   0.417   0.419   0.422
62    G         0.409   0.412   0.414   0.483   0.487   0.496   0.417   0.419   0.422
63    K         0.409   0.412   0.414  -0.901  -0.894  -0.838   0.417   0.419   0.422
64    K         0.409   0.412   0.414  -0.901  -0.894  -0.838   0.417   0.419   0.422
* gap fraction no less than  0.50; conservation set to M-S
  M: mean;  S: standard deviation

al2co - The parameters are:

Input alignment file - ../mafft-mac/clustal/Q3E764
Output conservation file - output/Q3E764
All 9 methods are used - true 
   1. unweighted entropy measure; 2. Henikoff entropy measure;
   3. independent count entropy measure;
   4. unweighted variance measure; 5. Henikoff variance measure;
   6. independent count variance measure;
   7. unweighted matrix-based sum-of-pairs measure;
   8. Henikoff matrix-based sum-of-pairs measure;
   9. independent count matrix-based sum-of-pairs measure;
Window size - 1
Conservation normalized to zero mean and unity variance
Gap fraction to suppress calculation -  0.50
